Even though he had lost the primaries, he had almost half the party supporting his candidacy and this led Balbina Herrera to nominate him as vice-presidential candidate in the PRD ticket for the 2009 presidential election.

In that election the PRD and Balbina Herrera lost to Ricardo Martinelli and Juan Carlos Varela by a wide margin.

This led Juan Carlos Navarro to call for all the National Executive Committee members to resign based on the poor election results.

In 2012, Juan Carlos Navarro was elected Secretary-General of the PRD, the top post in the party's structure.

For this reason, after the election Navarro negotiated a legislative pact called "Panama Primero" with president-elect Juan Carlos Varela to secure that many of the projects proposed during his campaign would become a reality.

Once the legislative pact was finalized, Navarro resigned his post as Secretary General of the PRD accepting his responsibility for the election results.

Navarro announced on August 21, 2018, that he was declining his aspirations to be chosen as the PRD's presidential candidate to back Ernesto Pérez Balladares in his bid to be the party's nominee.

In the story, Navarro said, "The only way to stop climate change is to involve the private and philanthropic sectors to deploy clean energy, electric mobility, conservation, and protection initiatives in Panama.